logo

1 Intro

This report provides some overall description of the database search. Users can use this to quickly check the overall quality of the experiment

2 Take-home figures

  • Peptide Sequences Identified in total: 31477

  • Avearge ms/ms identification rate(%): 32.73

  • Groups: KES; PBS; W

  • Groups: A; B

3 MSMS ID rate

Why you should pay attention to MSMS Id rate?

  1. MS ID rate is a good repretation of the MS run quality. Usually, raw files from Q-Exactive series should have roughly around 50% ms ID rate (Percentage of MSMS spectra identified as peptided, at a 1% FDR) for human cell culture digest, and at least 20% for metaproteomics samples according to experience. This number is a bit lower on QE- HFX and Exploris 480, because the scan rate is faster but the msms2 quality is not a bit lower

  2. MS ID rate should also be well-reproduced across samples and groupings.

  • Check the raw files if they have obnormally low ID rate, usually with abnormal LC/basepeak profile or low MS intensity.
  • A decreasing MS ID treand along sample running order indicates a performance drop of the MS: your MS might need to be cleaned. If the performance drops a lot, more than 20% within running time for the whole project, without scramble of the sample run-order, the data might not be usable, unless very careflly caliburated.

3.1 No Grouping

3.1.1 Scatter plot

3.1.2 Density plot

3.1.3 Box plot

3.2 Grouping: KES; PBS; W

3.2.1 Scatter plot

3.2.2 Density plot

3.2.3 Box plot

3.3 Grouping: A; B

3.3.1 Scatter plot

3.3.2 Density plot

3.3.3 Box plot

4 Peptide Sequence identified

4.1 No Grouping

4.1.1 Scatter plot

4.1.2 Density plot

4.1.3 Box plot

4.2 Grouping: KES; PBS; W

4.2.1 Scatter plot

4.2.2 Density plot

4.2.3 Box plot

4.3 Grouping: A; B

4.3.1 Scatter plot

4.3.2 Density plot

4.3.3 Box plot

5 Overall Performance

The overall performance for all raw files: